SABIO-RK is a curated database for biochemical reaction kinetics data. The system offers standardized data manually extracted from the literature or directly submitted from lab experiments. The captured data is standardized by the use of controlled vocabularies and annotations pointing to other resources and biological ontologies.

Computational approaches to study biochemistry require machine accessible representations of biochemical knowledge. Based on the requirements for assembling, managing and analysing genome-scale constraint-based models of liver metabolism we developed a semantic data model for representation of liver biochemical knowledge. Employing a role-based representation of biochemical processes as molecular events specified in the Web Ontology Language (OWL) we here outline an information model that employs
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ChemSpot is a named entity recognition tool for identifying mentions of chemicals in natural language texts, including trivial names, drugs, abbreviations, molecular formulas and IUPAC entities. Since the different classes of relevant entities have rather different naming characteristics, ChemSpot uses a hybrid approach combining a Conditional Random Field with a dictionary. It currently achieves an F1 measure of 74.2% on the SCAI corpus.
ChemSpot is released under the Common Public License 1.0.
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The expression of phosphoenolpyruvate carboxykinase 1 (PCK1) is stimulated by glucagon via cAMP-dependent activation and enhancement of binding of the transcription factor CREB to the CRE element in the PCK1 promoter. In primary cultured rat hepatocytes the pro-inflammatory cytokine interleukin-6 (IL6) inhibited the expression of PCK1 although the mode of action remained unclear so far. Binding of IL6 to its receptor initiates phosphorylation of several tyrosine residues of gp130 by Janus kinases
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Primary hepatocytes were exposed to a stimulus by exchanging culture medium, thereby simulating changes in the blood composition. The expression of genes at different time points was recorded. Differentially expressed genes were clustered using fuzzy c-means algorithm into five groups. The arcs of the possible network were identified using the NetGenerator algorithm under the restriction of biological knowledge. The analysis was restricted to the main metabolic pathways of hepatocytes. The reverse
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The BioCreative IV CHEMDNER Task provides participants with the opportunity to compare their methods for chemical named entity recognition (NER) and indexing in a controlled environment. We contributed to this task with our previous conditional random field based system [1] extended by a number of novel general and domain-speci c features. For the latter, we used features derived from two existing chemical NER systems, ChemSpot [2] and OSCAR [3], as well as various external resources. In this
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Recent successes have challenged the widely held belief that protein-protein interactions (PPIs) are 'undruggable'. We show that binding pockets defining PPIs and those that define protein-ligand interactions of currently marketed drugs are markedly different. In the case of PPIs, drug discovery methods that simultaneously target several small pockets at the protein-protein interface are likely to increase the chances of success in this new and important field of therapeutics.
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The Portal:
6 dimensions to organize content
easy information about difficult topics
quick and easy to publish the input
visibility to the public, colleagues and funders
presentation of the work of group

We investigate the influence of insulin, glucagon and epinephrine on the core metabolism of hepatocytes by means of a kinetic model. These hormones induce significant alterations in certain metabolic activities of key enzymes like Glycogen synthase and Glycogen phosphorylase. Insulin is the primary anabolic hormone promoting the storage of energy by stimulating, for example, the glycogen synthesis. The effect of Glucagon and epinephrine are opposite that of insulin. They cause the liver to convert
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We investigate the influence of insulin, glucagon and epinephrine on the core metabolism of hepatocytes by means of a kinetic model. These hormones induce significant alterations in certain metabolic activities of key enzymes like Glycogen synthase and Glycogen phosphorylase. Insulin is the primary anabolic hormone promoting the storage of energy by stimulating, for example, the glycogen synthesis. The effect of Glucagon and epinephrine are opposite that of insulin. They cause the liver to convert
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Motivation
The central carbon metabolism of the liver enables the remarkable homeostasis of numerous plasma metabolites under a wide variety of nutritional regimes and physiological states. Examples are the synthesis of glucose by gluconeogenesis and synthesis of ketone-body from fatty acids under fasting conditions or the postprandial storage of glucose and lipids in terms of glycogen and triglycerides.

Results
In order to better understand the regulatory mechanism accounting for the switch
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Background: One of the major challenges in complex multi-disciplinary systems biology projects is to understand and process data from a wide variety of data sources. Computational tools to assist in the analysis of this data are essential.
Method: LigDig is a web server designed to answer questions that previously required several independent queries to diverse data sources. It also performs basic manipulations and analyses of the structures of protein–ligand complexes. The LigDig webserver is
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This poster presents a sub-section of new results that were created within this Showcase. It's focus is on hepatic stellate cells (HSC). Unexpectedly, LPS reduced expression of the activation marker αSMA and other pro-fibrogenic genes in HSC, a finding which challenges the common hypothesis of LPS being an activator of quiescent HSC.

The cholesterol lowering drug atorvastatin (Lipitor) acts by inhibiting the enzyme HMGCoA reductase, which plays a central role in the production of cholesterol in the liver. To investigate the effects of atorvastatin on the central carbon metabolism and the bile acid synthesis we used rat hepatocyte as a model system and constructed a corresponding model based on HepatoNet1 and literature knowledge, e.g. the KEGG knowledgebase. To gain a high-quality model we fully balanced the model and checked
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Question: Liver regeneration is accomplished by the hepatocytes, which restore the liver mass after resection, trauma or toxic exposition provided that the insult does not affect the mitotic response of the hepatocytes. Parenchymal proliferation gives rise to progeny, which take over functional capacity. Yet, only limited knowledge is available on the time-dependent positional impact of regenerating hepatocytes ultimately determing the metabolic power of the liver as a whole. Therefore, it is
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The analysis of biological networks for interpreting data is becoming a standard in bioinformatics as it enables us to look at a process from the perspective of pathways and network modules rather than single proteins. To study proteins in the context of a cellular system, it is essential that the molecules with which a protein interacts are identified and the functional consequence of each interaction is understood.
We work on several aspects concerning data integration in protein interaction
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Question: NASH is a benign liver disease and will progress, if untreated, into fibrosis/cirrhosis and potentially into hepatocellular cancer. Human cell therapy approaches for the treatment of NASH have not been addressed yet. Therefore, the present work aimed at establishing an animal model to evaluate the feasibility of stem cell-derived hepatocytes in NASH.

Methods: Immundeficient Pfp/Rag2-/- mice were fed with a methionine-choline-deficient diet (MCD diet) for up to 5 weeks. Alanine-aminotransferase
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Question: NASH is a common clinical picture, mostly induced by the Western diet. In the long run NASH is a risk factor for cirrhosis and liver cancer (HCC), which ultimately requires liver transplantation. Because donor organs are limited cell transplantation is a new feasible therapeutic approach. Within this project we asked whether mice suffering from diet-induced NASH would benefit from transplanted adult stem cell-derived hepatocyte-like cells.
Methods: Immunodeficient mice obtained a
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Named entity recognition (NER) systems are often based on machine learning techniques to reduce the labor-intensive development of hand-crafted extraction rules and domain-dependent dictionaries. Nevertheless, time-consuming feature engineering is often needed to achieve state-of-the-art performance. In this study, we investigate the impact of such domain-specific features on the performance of recognizing and classifying mentions of pharmacological substances. We compare the performance of a
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Primary hepatocytes are a fundamental tool to investigate molecular mechanisms in liver physiopathology. Hepatocytes cultured on a 2D collagen
monolayer (CMS for sub-confluent and CMC for confluent) quickly de-differentiate, becoming apoptotic resistant and loosing canalicular polarity,
whereas when cultured on a 3D extracellular matrix (e.g. collagen sandwich, S) they can better sustain a differentiated state and form bile canaliculi
(BC) making the latter system feasible for using hepatocytes
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Background: The liver is an organ acting as a first line of defense against a number of pathological conditions including sepsis via an acute phase response (APR). Primary hepatocytes are a fundamental tool to fully understand the complex circuitry of signal transduction and gene regulation in APR. However, it is known that primary hepatocytes undergo a dedifferentiation process, i.e., apoptotic resistance and epithelial to mesenchymal transition. These alterations are being partly repressed in
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